Did you manually remove the cache files, or just use the Clean button in Preferences? Pr won't (or at least, shouldn't) trash cache files for media that is online--that's what the Media Cache Database tracks. You can move your media files or change the folder name temporarily, and then use the Clean function; that will usually trick Pr into trashing the cache files for those clips, since its only following them based on their original paths.

This suggests why some clips show up properly, but others do not. If it was a display driver issue, it would be all your clips.

Will the clips show up alright in CS5.5, assuming you have it installed alongside CS6? I still say this is a caching issue; I've had the same problem before, though that was going from CS5 to CS5.5 with the same type of footage.

OK, do you have MPEG StreamClip? If not, Google it up and download it; it's free. Open one of the clips showing the problem in MPEG StreamClip, and then go to File > Save As, and then pick a new name for the file and save it. Try importing this clip into CS6 and see what happens...

(You can also do this with QT Pro, if you already have that installed. QT Player won't do it, which is why I suggested MPEG Stream Clip.)

What you're seeing looks like what happens when there is a mis-translation between YUV and RGB (green and pink from black and rowbytes errors). Something rather odd is happening. I can't see this having anything to do with your graphics hardware, but I can totally see it being caused by a damaged or otherwise 'unexpected' form of file. Since PPro can handle H.264 files (they are .mov internally regardless of their extension) 'natively' (meaning that it doesn't have to use Quicktime to read them), it makes me wonder - is the same rendering you're seeing the same on all of the files from your 5dMarkII, or just this one?